[English] 日本語
Yorodumi
- PDB-3oyp: HCV NS3/4A in complex with ligand 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oyp
TitleHCV NS3/4A in complex with ligand 3
Components
  • Non-structural protein 4A
  • Peptidomimetic inhibitor
  • Serine protease NS3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / NS3 / NS4A / HEPATITIS C VIRUS / PROTEASE INHIBITION / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


RNA stabilization / DNA/DNA annealing activity / RNA strand annealing activity / RNA folding chaperone / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint ...RNA stabilization / DNA/DNA annealing activity / RNA strand annealing activity / RNA folding chaperone / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / protein-DNA complex / nucleoside-triphosphate phosphatase / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily ...Thrombin, subunit H - #120 / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Trypsin-like serine proteases / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Thrombin, subunit H / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
N-propanoyl-D-alanyl-(4R)-4-[(7-bromoisoquinolin-1-yl)oxy]-N-{(1R,2R)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-L-prolinamide / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.76 Å
AuthorsHagel, M. / Niu, D. / St.Martin, T. / Sheets, M.P. / Qiao, L. / Bernard, H. / Karp, R.M. / Zhu, Z. / Labenski, M.T. / Chaturvedi, P.C. ...Hagel, M. / Niu, D. / St.Martin, T. / Sheets, M.P. / Qiao, L. / Bernard, H. / Karp, R.M. / Zhu, Z. / Labenski, M.T. / Chaturvedi, P.C. / Nacht, M. / Westlin, W.F. / Petter, R.C. / Singh, J.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Selective irreversible inhibition of a protease by targeting a noncatalytic cysteine.
Authors: Hagel, M. / Niu, D. / St.Martin, T. / Sheets, M.P. / Qiao, L. / Bernard, H. / Karp, R.M. / Zhu, Z. / Labenski, M.T. / Chaturvedi, P. / Nacht, M. / Westlin, W.F. / Petter, R.C. / Singh, J.
History
DepositionSep 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Dec 19, 2012Group: Non-polymer description / Structure summary
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.6Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine protease NS3
B: Serine protease NS3
C: Non-structural protein 4A
D: Non-structural protein 4A
E: Peptidomimetic inhibitor
F: Peptidomimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3558
Polymers44,2246
Non-polymers1312
Water18010
1
A: Serine protease NS3
C: Non-structural protein 4A
E: Peptidomimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1123
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-48 kcal/mol
Surface area8270 Å2
MethodPISA
2
B: Serine protease NS3
D: Non-structural protein 4A
F: Peptidomimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1784
Polymers22,1123
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-47 kcal/mol
Surface area8190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.401, 94.401, 83.129
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Serine protease NS3 / Hepacivirin / NS3P / p70


Mass: 19749.553 Da / Num. of mol.: 2
Fragment: PROTEASE/HELICASE NS3 (P70), UNP residues 1027-1213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus (isolate Japanese) / Production host: Escherichia coli (E. coli)
References: UniProt: P26662, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Protein/peptide Non-structural protein 4A / NS4A / p8


Mass: 1686.097 Da / Num. of mol.: 2
Fragment: NONSTRUCTURAL PROTEIN NS4A (P4), UNP residues 1677-1991
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus (isolate Japanese) / Production host: Escherichia coli (E. coli) / References: UniProt: P26662
#3: Protein/peptide Peptidomimetic inhibitor


Type: Peptide-like / Class: Antiviral / Mass: 676.579 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: N-propanoyl-D-alanyl-(4R)-4-[(7-bromoisoquinolin-1-yl)oxy]-N-{(1R,2R)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-L-prolinamide
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.11 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: NaCl, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: PILATUS 6M / Detector: CCD / Date: Dec 4, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.76→81.65 Å / Num. all: 10926 / Num. obs: 10926 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.123
Reflection shellResolution: 2.76→2.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.643 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: 1DXP

1dxp


Resolution: 2.76→81.65 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.849 / SU B: 16.216 / SU ML: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 762 7 %RANDOM
Rwork0.21483 ---
all0.22271 10158 --
obs0.21892 10158 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.76→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 2 10 2827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222878
X-RAY DIFFRACTIONr_bond_other_d0.0050.022687
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.0113934
X-RAY DIFFRACTIONr_angle_other_deg3.42736224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.59221.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94315436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5511524
X-RAY DIFFRACTIONr_chiral_restr0.0560.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_nbd_refined0.1810.2574
X-RAY DIFFRACTIONr_nbd_other0.1760.22707
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21417
X-RAY DIFFRACTIONr_nbtor_other0.0820.21647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.320.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1450.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.19522362
X-RAY DIFFRACTIONr_mcbond_other0.1562772
X-RAY DIFFRACTIONr_mcangle_it1.51432984
X-RAY DIFFRACTIONr_scbond_it2.19441213
X-RAY DIFFRACTIONr_scangle_it3.0356938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.76→2.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 67 -
Rwork0.311 738 -
obs--99.88 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more